BMC Biophysics | Structural stability and dynamics section

1.

Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies

Anke Steinbach, Christine K Maurer, Elisabeth Weidel, Claudia Henn, Christian Brengel, Rolf W Hartmann, Matthias Negri BMC Biophysics 2013, 6:10 (1 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

2.

Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations

Haina Qin, Liangzhong Lim, Jianxing Song BMC Biophysics 2012, 5:2 (25 January 2012)

Structural determination of the EphA4 ligand binding domain provides the first experimental and computational evidence that intrinsic dynamics are most likely to be responsible for the observed high conformational diversity that mediates binding affinity and specificity.

3.

An upper limit for macromolecular crowding effects

Andrew C Miklos, Conggang Li, Courtney D Sorrell, L Andrew Lyon, Gary J Pielak BMC Biophysics 2011, 4:13 (31 May 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Synthetic microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.

4.

Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

Yu-ming M Huang, Chia-en A Chang BMC Biophysics 2011, 4:12 (25 May 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Mechanism of phosphothreonine/serine recognition and specificity is elucidated for three well-known phosphopeptide-binding domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated domain (FHA) with the use of molecular dynamics simulations.

5.

Diffusion of hydrophobin proteins in solution and interactions with a graphite surface

Paolo Mereghetti, Rebecca C Wade BMC Biophysics 2011, 4:9 (21 April 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Hydrophobins, the most powerful surface-active proteins known, exist in solution as a mixture of monomers in equilibrium with different types of oligomers but in contact with a graphite layer they form tetramers and accumulate close to the hydrophobic surface.

6.

Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package

Tihamér Geyer BMC Biophysics 2011, 4:7 (13 April 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

A new "brownmove" simulation package designed for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes combines Brownian and Langevin Dynamics propagation with fast hydrodynamics, a flexible protein model and interfaces for "open" simulation settings.

7.

Gated Diffusion-controlled Reactions

J Andrew McCammon BMC Biophysics 2011, 4:4 (2 March 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Andy McCammon discusses both the protein-centric and detailed dynamic simulation methods that have been applied to predict rates of ligand binding and reactivity at protein active sites and the biological implications of these findings.

8.

Diffusion in crowded biological environments: applications of Brownian dynamics

Maciej Długosz, Joanna Trylska BMC Biophysics 2011, 4:3 (2 March 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Maciej Dlugosz and Joanna Trylska review recent developments in particle-based Brownian dynamics algorithms and their application to model diffusive transport in crowded systems, which are proving useful in improving our understanding of metabolism, transport and signaling.

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	1.	Research article Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies Anke Steinbach, Christine K Maurer, Elisabeth Weidel, Claudia Henn, Christian Brengel, Rolf W Hartmann, Matthias Negri BMC Biophysics 2013, 6:10 (1 August 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	2.	Research article Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations Haina Qin, Liangzhong Lim, Jianxing Song BMC Biophysics 2012, 5:2 (25 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Structural determination of the EphA4 ligand binding domain provides the first experimental and computational evidence that intrinsic dynamics are most likely to be responsible for the observed high conformational diversity that mediates binding affinity and specificity.
	3.	Research article An upper limit for macromolecular crowding effects Andrew C Miklos, Conggang Li, Courtney D Sorrell, L Andrew Lyon, Gary J Pielak BMC Biophysics 2011, 4:13 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Synthetic microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
	4.	Research article Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics Yu-ming M Huang, Chia-en A Chang BMC Biophysics 2011, 4:12 (25 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mechanism of phosphothreonine/serine recognition and specificity is elucidated for three well-known phosphopeptide-binding domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated domain (FHA) with the use of molecular dynamics simulations.
	5.	Research article Diffusion of hydrophobin proteins in solution and interactions with a graphite surface Paolo Mereghetti, Rebecca C Wade BMC Biophysics 2011, 4:9 (21 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hydrophobins, the most powerful surface-active proteins known, exist in solution as a mixture of monomers in equilibrium with different types of oligomers but in contact with a graphite layer they form tetramers and accumulate close to the hydrophobic surface.
	6.	Research article Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package Tihamér Geyer BMC Biophysics 2011, 4:7 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new "brownmove" simulation package designed for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes combines Brownian and Langevin Dynamics propagation with fast hydrodynamics, a flexible protein model and interfaces for "open" simulation settings.
	7.	Review Gated Diffusion-controlled Reactions J Andrew McCammon BMC Biophysics 2011, 4:4 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Andy McCammon discusses both the protein-centric and detailed dynamic simulation methods that have been applied to predict rates of ligand binding and reactivity at protein active sites and the biological implications of these findings.
	8.	Review Diffusion in crowded biological environments: applications of Brownian dynamics Maciej Długosz, Joanna Trylska BMC Biophysics 2011, 4:3 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Maciej Dlugosz and Joanna Trylska review recent developments in particle-based Brownian dynamics algorithms and their application to model diffusive transport in crowded systems, which are proving useful in improving our understanding of metabolism, transport and signaling.